selectVar: Selecting variables (genes) from result of MCIA or CIA...

In omicade4: Multiple co-inertia analysis of omics datasets

Description

The user level function calls selectVar.mcia or selectVar.cia. Function cia or mcia projects variables (genes) from different datasets to a 2 dimensional space. This function supplies a method selecting variables (genes) according to the coordinates of variables

Usage

  selectVar(x, axis1 = 1, axis2 = 2, ...)

Arguments

x	An object of class cia or mcia, the result returned by cia or mcia respectively.
axis1	Integer, the column number for the x-axis. The default is 1.
axis2	Integer, the column number for the y-axis. The default is 2.
...	Other arguments

Value

Returns a data.frame describing which variables (genes) are presented on which data.frames within the limited region(s).

Author(s)

Chen Meng

See Also

See Also as selectVar.mcia, selectVar.cia

Examples

data(NCI60_4arrays)
mcoin <- mcia(NCI60_4arrays)
selectVar(mcoin, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf))

# an example for the usage of sepID.data and sepID.sep
nci60_mod <- NCI60_4arrays
rownames(nci60_mod$hgu95) <- paste(rownames(nci60_mod$hgu95), "s1", sep="_")
mcoin_mod <- mcia(nci60_mod)
# without specifing
selectVar(mcoin_mod, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf))
# specifing the sepID.data and sepID.sep
selectVar(mcoin_mod, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf), sepID.data=4, sepID.sep="_")

omicade4 documentation built on Nov. 8, 2020, 7:47 p.m.